- scirpy.io.read_bd_rhapsody(path, dominant=False)
Read IR data from the BD Rhapsody Analysis Pipeline.
*_VDJ_Unfiltered_Contigs.csvfiles. The applicable filename depends your version of the BD Rhapsody pipeline.
More recent versions of the pipeline generate data in standardized AIRR Rearragement format. If you have a chance to do so, we recommend reanalysing your data with the most recent version of the BD Rhapsody pipeline and read output filese with
*_perCellfiles are currently not supported, follow the IO Tutorial to import custom formats and make use of this snippet
- Reading data into Scirpy has the following constraints:
Each cell can have up to four productive chains chains (Dual IR): two VJ and two VDJ chains.
Excess chains are ignored (those with lowest read count/UMI count) and cells flagged as Multichain-cell.
Non-productive chains are ignored.
Chain loci must be valid IMGT locus names.
Excess chains, non-productive chains, chains without a CDR3 sequence, or chains with invalid loci are serialized to JSON and stored in the
extra_chainscolumn. They are not used by scirpy except when exporting the
AnnDataobject to AIRR format.
For more information, see Immune receptor (IR) model.